Locking size of individual mesh part
After scaling the object, determine the amount of scaling of the holes required to "undo" that scaling. For example, if the object was scaled down by a factor of 0.9, use 1 / 0.9 = 1.111 as the scale factor to adjust the holes by. 

To quickly scale all of the holes switch to use the pivot center "Individual Origins" and it should scale each hole separately.

You can get the add-on presented in this answer to verify that the dimensions of the holes are indeed the same: https://blender.stackexchange.com/a/68678/28015.